pysimm.calc

Module Contents

pysimm.calc.np

pysimm.calc.intersection(line1, line2)

pysimm.calc.intersection

Finds intersection between two 2D lines given by two sets of points

Parameters:

• line1 – [[x1,y1], [x2,y2]] for line 1
• line2 – [[x1,y1], [x2,y2]] for line 2

Returns:

x,y intersection point

pysimm.calc.find_rotation(a, b)

pysimm.calc.find_rotation

Finds rotation vector required to align vector a and vector b

Parameters:

• a – 3D vector [x,y,z]
• b – 3D vector [x,y,z]

Returns:

rotation matrix

pysimm.calc.rotate_vector(x, y, z, theta_x=None, theta_y=None, theta_z=None)

pysimm.calc.rotate_vector

Rotates 3d vector around x-axis, y-axis and z-axis given by user defined angles

Parameters:

• x – x vector component
• y – y vector component
• z – z vector component
• theta_x – angle to rotate vector around x axis
• theta_y – angle to rotate vector around y axis
• theta_z – angle to rotate vector around z axis

Returns:

new vector [x,y,z]

pysimm.calc.distance(p1, p2)

pysimm.calc.distance

Finds distance between two Particle objects. Simply calculates length of vector between particle coordinates and does not consider periodic boundary conditions.

Parameters:

• p1 – Particle
• p2 – Particle

Returns:

distance between particles

pysimm.calc.angle(p1, p2, p3, radians=False)

pysimm.calc.angle

Finds angle between three Particle objects. Does not consider periodic boundary conditions.

Parameters:

• p1 – pysimm.system.Particle
• p2 – pysimm.system.Particle
• p3 – pysimm.system.Particle
• radians – returns value in radians if True (False)

Returns:

angle between particles

pysimm.calc.dihedral(p1, p2, p3, p4, radians=False)

pysimm.calc.chiral_angle(a, b, c, d)

pysimm.calc.chiral_angle

Finds chiral angle between four Particle objects. Chiral angle is defined as the angle between the vector resulting from vec(a->c) X vec(a->d) and vec(a->b). Used to help define tacticity where backbone follow b’–a–b and c and d are side groups.

b’–a–b

/ c d

Parameters:

• a – pysimm.system.Particle
• b – pysimm.system.Particle
• c – pysimm.system.Particle
• d – pysimm.system.Particle

Returns:

chiral angle

pysimm.calc.tacticity(s, a_tag=None, b_tag=None, c_tag=None, d_tag=None, offset=None, return_angles=True, unwrap=True, rewrap=True, skip_first=False)

pysimm.calc.tacticity

Determines tacticity for polymer chain. Iterates through groups of four patricles given by X_tags, using offset. This assumes equivalent atoms in each group of four are perfectly offset.

Parameters:

• s – System
• a_tag – tag of first a particle
• b_tag – tag of first b particle
• c_tag – tag of first c particle
• d_tag – tag of first d particle
• offset – offset of particle tags (monomer repeat atomic count)
• return_angles – if True return chiral angles of all monomers
• unwrap – True to perform unwrap before calculation (REQUIRED before calculation, but not required in this
• function) –
• rewrap – True to rewrap system after calculation
• skip_first – True to skip first monomer (sometime chirality is poorly defined for thsi monomer)

Returns:

tacticity or tacticity, [chiral_angles]

pysimm.calc.frac_free_volume(v_sp, v_void)

pysimm.calc.frac_free_volume

Determines fractional free volume for a poroous system.

Parameters:

• v_sp – specific volume
• v_void – void volume

Returns:

fractional free volume

pysimm.calc.pbc_distance(s, p1, p2)

pysimm.calc.pbc_distance

Calculates distance between particles using PBC

Parameters:

• s – System
• p1 – Particle
• p2 – Particle

Returns:

distance between particles

pysimm.calc.LJ_12_6(pt, d)

pysimm.calc.LJ_9_6(pt, d)

pysimm.calc.buckingham(pt, d)

pysimm.calc.harmonic_bond(bt, d)

pysimm.calc.class2_bond(bt, d)

pysimm.calc.harmonic_angle(at, d)

pysimm.calc.class2_angle(at, d)

pysimm.calc.harmonic_dihedral(dt, d)

pysimm.calc.class2_dihedral(dt, d)

pysimm.calc.opls_dihedral(dt, d)

pysimm.calc.fourier_dihedral(dt, d)

pysimm.calc.harmonic_improper(it, d)

pysimm.calc.cvff_improper(it, d)

pysimm.calc.umbrella_improper(it, d)